package jalview.bin;
+import jalview.gui.Preferences;
+
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
{
private final static String[] params = { "alignpdbfiles",
- "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN", "annotations",
+ Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
+ "annotations",
"APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
"debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
"embedded", "enableSplitFrame", "externalstructureviewer", "features",
String arg = args[i].trim();
if (arg.startsWith("name="))
{
- String key = getAttr(arg, "name");
+ String prefName = getAttr(arg, "name");
+ String appletName = prefName.toLowerCase();
+ String argName = prefName;
String value = getAttr(arg, "value");
- String name = key;
- switch (name)
+
+ // note that Application arguments ARE case-sensitive, but
+ // Applet.getParameter() is not.
+
+ switch (appletName)
{
- case "alignpdbfiles":
- break;
- case "annotationcolour_max":
- name = "ANNOTATIONCOLOUR_MAX";
- break;
- case "annotationcolour_min":
- name = "ANNOTATIONCOLOUR_MIN";
- break;
- case "annotations":
- value = checkTF(value);
+
+ case "file":
+ argName = "open";
+ appletName = null;
+ value = resourcePath + value;
break;
- case "application_url":
- name = "APPLICATION_URL";
+ case "file2":
+ argName = "open2";
+ prefName = null;
+ value = resourcePath + value;
break;
- case "automaticscrolling":
- name = "automaticScrolling";
+ case "features":
+ case "jnetfile":
+ case "jpredfile":
+ case "pdbfile":
+ case "scorefile":
+ case "sequence":
+ // setting argName to null indicates that we want
+ // JalviewAppLoader to take care of this.
+ prefName = argName = null;
+ value = resourcePath + value;
break;
- case "centrecolumnlabels":
+ case "tree":
+ case "treefile":
+ // setting appletName to null indicates that we want
+ // Jalview.doMain to taken care of this as Jalview args
+ argName = "tree";
+ appletName = null;
+ value = resourcePath + value;
break;
+
+ // non-loading preferences
+
case "defaultcolour":
- name = "defaultColour";
+ prefName = Preferences.DEFAULT_COLOUR;
break;
case "defaultcolournuc":
- name = "defaultColourNuc";
+ prefName = Preferences.DEFAULT_COLOUR_NUC;
break;
case "defaultcolourprot":
- name = "defaultColourProt";
- break;
- case "enablesplitframe":
- name = "enableSplitFrame";
+ prefName = Preferences.DEFAULT_COLOUR_PROT;
break;
- case "externalstructureviewer":
- break;
- case "features":
- value = resourcePath + value;
- break;
- case "format":
+ case "annotationcolour_max":
+ prefName = Preferences.ANNOTATIONCOLOUR_MAX;
break;
- case "heightscale":
- name = "heightScale";
+ case "annotationcolour_min":
+ prefName = Preferences.ANNOTATIONCOLOUR_MIN;
break;
- case "hidefeaturegroups":
+ case "enablesplitframe":
+ prefName = Preferences.ENABLE_SPLIT_FRAME;
break;
- case "jalviewhelpurl":
+ case "centrecolumnlabels":
+ prefName = Preferences.CENTRE_COLUMN_LABELS;
break;
- case "jnetfile":
- value = resourcePath + value;
+ case "sortby":
+ prefName = Preferences.SORT_ALIGNMENT; // id, etc.
break;
- case "jpredfile":
- value = resourcePath + value;
+ case "normalisesequencelogo":
+ prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
break;
- case "label":
+ case "relaxedidmatch":
+ prefName = Preferences.RELAXEDSEQIDMATCHING;
break;
- case "linklabel_":
- name = "linkLabel_";
+ case "scaleproteinascdna":
+ prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
break;
- case "linklabel_1":
- name = "linkLabel_1";
+ case "userdefinedcolour":
+ argName = "colour";
+ prefName = Preferences.USER_DEFINED_COLOURS;
break;
- case "linkurl_":
- name = "linkURL_";
+ case "wrap":
+ prefName = Preferences.WRAP_ALIGNMENT;
break;
- case "nojmol":
+
+ // implemented; not tested:
+
+ case "oninit":
+ prefName = null;
break;
- case "normaliselogo":
- name = "normaliseLogo";
+ case "annotations":
+ value = resourcePath + value;
+ argName = null;
break;
- case "normalisesequencelogo":
- name = "normaliseSequenceLogo";
+ case "hidefeaturegroups":
+ // TODO
break;
- case "oninit":
+ case "pdbseq":
+ argName = prefName = null;
break;
- case "pdbfile":
- name = "PDBFILE";
+ case "sortbytree":
+ prefName = Preferences.SORT_BY_TREE;
+ value = checkTF(value);
+ appletName = null; // taken care of by Jalview
break;
- case "pdbseq":
- name = "PDBSEQ";
+ case "format":
break;
- case "relaxedidmatch":
+ case "alignpdbfiles":
+ argName = prefName = null;
break;
- case "resolvetocodebase":
+ case "separator":
break;
+
+ // TODO: probably not relevant?
+
case "rgb":
- name = "RGB";
+ prefName = null; // TODO no background for application?
break;
- case "scaleproteinascdna":
- name = "scaleProteinAsCdna";
+ case "externalstructureviewer":
break;
- case "scorefile":
- name = "scoreFile";
- value = resourcePath + value;
+ case "application_url":
break;
- case "separator":
+ case "automaticscrolling":
break;
- case "sequence":
+ case "heightscale":
break;
- case "sortby":
- name = "sortBy";
+ case "jalviewhelpurl":
break;
- case "sortbytree":
- value = checkTF(value);
- key = null; // taken care of by Jalview
+ case "label":
break;
- case "tree":
- case "treefile":
- name = "tree";
- value = resourcePath + value;
- key = null; // taken care of by Jalview
+ case "linklabel_":
+ prefName = "linkLabel_";
break;
- case "uppercase":
- name = "upperCase";
+ case "linklabel_1":
+ prefName = "linkLabel_1";
break;
- case "userdefinedcolour":
- name = "userDefinedColour";
+ case "linkurl_":
+ prefName = "linkURL_";
break;
+
+ // unknown:
+
+ case "nojmol":
+ case "normaliselogo":
+ case "resolvetocodebase":
+ case "uppercase":
case "widthscale":
- name = "widthScale";
- break;
case "windowheight":
- name = "windowHeight";
- break;
case "windowwidth":
- name = "windowWidth";
- break;
- case "wrap":
+ argName = prefName = null;
break;
- // cases not handled in doc/parameters.xlsx
+ // TRUE/FALSE
+
case "debug":
value = checkTF(value);
break;
- case "file":
- name = "open";
- value = resourcePath + value;
- break;
- case "file2":
- value = resourcePath + value;
- break;
case "embedded":
value = checkTF(value);
break;
- case "showannotation":
- name = "SHOW_ANNOTATIONS";
+ case "showbutton":
value = checkTF(value);
break;
- case "showbutton":
+ case "showannotation":
+ prefName = Preferences.SHOW_ANNOTATIONS;
value = checkTF(value);
break;
case "showconsensus":
- name = "SHOW_CONSENSUS_LOGO";
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
value = checkTF(value);
break;
case "showconsensushistogram":
- name = "SHOW_CONSENSUS_HISTOGRAM";
+ prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
value = checkTF(value);
break;
case "showconservation":
- name = "SHOW_CONSERVATION";
+ prefName = Preferences.SHOW_CONSERVATION;
value = checkTF(value);
break;
- case "showfeaturegroups":
+ case "showgroupconsensus":
+ prefName = Preferences.SHOW_GROUP_CONSENSUS;
value = checkTF(value);
break;
- case "showfeaturesettings":
- name = "showFeatureSettings";
+ case "showgroupconservation":
+ prefName = Preferences.SHOW_GROUP_CONSERVATION;
value = checkTF(value);
break;
- case "showfullid":
- name = "showFullId";
+ case "showoccupancy":
+ prefName = Preferences.SHOW_OCCUPANCY;
value = checkTF(value);
break;
- case "showgroupconsensus":
- name = "SHOW_GROUP_CONSENSUS";
+ case "showquality":
+ prefName = Preferences.SHOW_QUALITY;
value = checkTF(value);
break;
- case "showgroupconservation":
- name = "SHOW_GROUP_CONSERVATION";
+ case "showsequencelogo":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
value = checkTF(value);
break;
- case "showoccupancy":
- name = "SHOW_OCCUPANCY";
+ case "showfeaturegroups":
value = checkTF(value);
break;
- case "showquality":
- name = "SHOW_QUALITY";
+ case "showfeaturesettings":
value = checkTF(value);
break;
- case "showsequencelogo":
- name = "showSequenceLogo";
+ case "showfullid":
value = checkTF(value);
break;
case "showtreebootstraps":
- name = "showTreeBootstraps";
value = checkTF(value);
break;
case "showtreedistances":
- name = "showTreeDistances";
value = checkTF(value);
break;
case "showunconserved":
- name = "showUnconserved";
+ prefName = Preferences.SHOW_UNCONSERVED;
value = checkTF(value);
break;
case "showunlinkedtreenodes":
- name = "showUnlinkedTreeNodes";
value = checkTF(value);
break;
default:
+ if (appletName.startsWith("pdbfile")
+ || appletName.startsWith("sequence") && Character.isDigit(
+ appletName.charAt(appletName.length() - 1)))
+ {
+ // could be pdbFile2, for example
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+ }
+ // or one of the app preference names
break;
}
- if (value != null)
+ // put name and value into application args
+ if (value != null && argName != null)
{
- vargs.add(name);
+ vargs.add(argName);
if (value != "true")
{
vargs.add(value);
{
value = "false";
}
- System.out.println("AppletParams name=" + name + " value=" + value);
- Cache.setPropertyNoSave(name, value);
- if (key != null)
+ System.out.println("AppletParams propName=" + prefName + " argName="
+ + argName + " appletName="
+ + appletName + " value=" + value);
+ if (appletName != null)
+ {
+ appletParams.put(appletName, value);
+ }
+ if (prefName != null)
{
- appletParams.put(key, value);
+ Cache.setPropertyNoSave(prefName, value);
}
}
}
git://source.jalview.org / jalview.git / blobdiff